Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio ( RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.

Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Funneled landscape leads to robustness of cellular networks: MAPK signal transduction

We uncover the underlying potential energy landscape for a cellular network. We find that the potential energy landscape of the mitogen-activated protein-kinase signal transduction network is funneled toward the global minimum. The funneled landscape is quite robust against random perturbations. This naturally explains robustness from a physical point of view. The ratio of slope versus roughness of the landscape becomes a quantitative measure of robustness of the network. Funneled landscape is a realization of the Darwinian principle of natural selection at the cellular network level. It provides an optimal criterion for network connections and design. Our approach is general and can be applied to other cellular networks.

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

We study the nature of biomolecular binding. We found that in general there exists several thermodynamic phases: a native binding phase, a non-native phase, and a glass or local trapping phase. The quantitative optimal criterion for the binding specificity is found to be the maximization of the ratio of the binding transition temperature versus the trapping transition temperature, or equivalently the ratio of the energy gap of binding between the native state and the average non-native states versus the dispersion or variance of the non-native states. This leads to a funneled binding energy landscape.

Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We found that the first passage-time (FPT) distribution undergoes a dynamic transition at a temperature below which the FPT distribution develops a power-law tail, a signature of the intermittent nonexponential kinetic phenomena for the folding dynamics. Possible applications to single-molecule dynamics experiments are discussed.

Report on some species of Palaemonidae (Crustacea, Decapoda) from French Polynesia

Based on material collected from French Polynesia and deposited in the Museum national d'Histoire naturelle, Paris, the present paper reports 31 palaemonid shrimp species, which belong to the Palaemoninae (two genera, three species) and to the Pontoniinae (12 genera, 28 species), including six new species. The new species are: Izucaris crosnieri n. sp., Periclimenes alexanderi n. sp., P. josephi n. sp., P platydactylus n. sp., P polynesiensis n. sp. and P vicinus n. sp. Detailed descriptions and illustrations of the new species are provided. Besides the six new species, ten other species are recorded for the first time from French Polynesia: Exoclimenella maldivensis Duris & Bruce, 1995, Kemponia rapanui (Fransen, 1987) n. comb., Palaemonella crosnieri Bruce, 1978, P spinulata Yokoya, 1936, Periclimenaeus hecate (Nobili, 1904), P orbitocarinatus Fransen, 2006, Periclimenes aleator Bruce, 199 1, P paralcocki Li & Bruce, 2006, P uniunguiculatus Bruce, 1990, Pontonides loloata Bruce, 2005.

Genetic diversity of the subterranean Gansu zokor in a semi-natural landscape

We studied the relationship between genetic diversity of the subterranean Gansu zokor Myospalax cansus and habitat variability in the Loess Plateau, Qinghai Province, China. We used a combination of geographic information systems and molecular techniques to assess the impact of habitat composition and human activities on the genetic diversity of zokor populations in this semi-natural landscape. Although they occurred relatively infrequently in the landscape, woodland and high-coverage grassland habitats were the main positive contributors to the genetic diversity of zokor populations. Rural residential land, plain agricultural land and low-coverage grassland had a negative effect on genetic diversity. Hilly agricultural land and middle-coverage grassland had little impact on zokor genetic diversity. There were also interactions between some habitat types, that is, habitat types with relatively better quality together promoted conservation of genetic diversity, while the interaction between (among) bad habitat types made situations worse. Finally, habitat diversity, measured as patch richness and Shannon's diversity index, was positively correlated with the genetic diversity. These results demonstrated that: (1) different habitat types had different effects on the genetic diversity of zokor populations and (2) habitat quality and habitat heterogeneity were important in maintaining genetic diversity. Habitat composition was closely related to land use thus emphasizing the importance of human activities on the genetic diversity of subterranean rodent populations in this semi-natural landscape. Although the Gansu zokor was considered to be a pest species in the Loess Plateau, our study provides insights for the management and conservation of other subterranean rodent species.

Strategic intelligence, Counter-Intelligence and Alliance Diplomacy in Anglo-French relations before the Second World War

Jackson, Peter, and Joe Maiolo, 'Strategic intelligence, Counter-Intelligence and Alliance Diplomacy in Anglo-French relations before the Second World War', Military History (2006) 65(2) pp.417-461 RAE2008

Faith in the Landscape : Overseas Pilgrimages in 'The Book of Margery Kempe'

Watt, D. (2006). Faith in the Landscape: Overseas Pilgrimages in 'The Book of Margery Kempe'. In C. Lees and G. Overing (Eds.), A Place to Believe In: Locating Medieval Landscapes (pp.170-187). University Park (PA): Pennsylvania State University Press. RAE2008

In Comes I: Performance, Memory and Landscape

Pearson, Mike, In Comes I: Performance, Memory and Landscape (Exeter: University of Exeter Press, 2007) RAE2008

The French Second Empire: an anatomy of political power

Price, Roger, The French Second Empire: an anatomy of political power (Cambridge: Cambridge University Press, 2001), pp.x+507 RAE2008

Iolo Morganwg and the Welsh rural landscape

Jones, David. 'Iolo Morganwg and the Welsh rural landscape', In: A rattleskull genius: the many faces of Iolo Morganwg (Cardiff: University of Wales Press, 2005), pp.227-250 RAE2008

Developing the untapped wealth of Britain's ?Celtic Fringe? : Water engineering and the Welsh landscape, 1870 ? 1960

Roberts, O. (2006). Developing the untapped wealth of Britain's ?Celtic fringe?: water engineering and the Welsh landscape, 1870-1960. Landscape Research. 31(2), pp.121-133. RAE2008